The Doctor was summoned to Greenwich Park by Martha and Captain Magambo who claimed that the trees were moving, three people were ingested by them and the trunks were marked with Enochian symbols, a language invented by mathematician and magician John Dee to converse with angels. The Doctor realises the "angels" were trapped beneath the observatory for four hundred years, but emerged through the trees in the park. While he sent Martha and Matthew to investigate Crane's house, the Doctor, Emily and gardener Mr Crane headed into the passages beneath the park to communicate with the "angels", in actual fact aliens waiting in suspended animation for the Doctor to come and take them home. With a UNIT soldier, Martha and Matthew searched Mr Crane's house. Matthew discovered a sketch of the Advocate, but the soldier took it from him, urging caution in his dealings with the Doctor. The soldier was really the Gizou in disguise. Martha, meanwhile, discovered an alien dossier on the Doctor and realised he was set up. Believing the Enochai's story, the Doctor set them free, but it was a trick. John Dee trapped them, but they became free to take over all of the trees and claim the Earth.

The Enochia realised the Doctor didn't remove the forcefield trapping it and ordered Crane to shoot Emily. The Doctor and Emily escaped but plunged down a hidden shaft into an ancient cavern where they discovered a stripped down colony ship containing thousands of Enochians in stasis. A holographic projection of John Dee informed them that the Enochians were energy beings who planned conquest. Emily escaped to the surface but Crane caught the Doctor and the Enochian ordered his imprisonment. The Advocate arrived and opened the stasis pods, releasing the Enochia. The trees drove UNIT back, but the situation became even worse as the Enochia flooded out of the ground.

The angels trapped Central London in a forcefield. A battle with UNIT began, leaving UNIT seriously outgunned. The Doctor spoke to one of the angels and realised it was the Gizou in disguise. The Gizou revealed that the whole scheme was a set-up. The Advocate appeared to Martha and the trapped humans and proposed a way of ending the crisis, by striking at the Enochian ship. Crane, who overheard the Gizou, rescued the Doctor. Martha, meanwhile, escaped the bunker, found Emily and, with the help of the Knights Arboretum, a select group of gardeners of which Crane was once a member, was reunited with the Doctor. Returning to the bunker, the Doctor confronted the Advocate, but Magambo refused to allow him time to develop an alternative solution to the Enochia threat and insisted on following the Advocate's plan. She arrested the Doctor.

With the help of the Knights Arboretum, Martha and Emily rescued the Doctor. Mr Crane, meanwhile, returned to the ship on a suicide mission to destroy it. The Doctor arrived and launched the ship into space, which drew all the energy creatures up with it. The Advocate's bomb was no longer needed, but the countdown was accidentally started. Mr Crane spotted it in the nick of time, but if he rose his finger from the button, the ship would explode. The Doctor could do nothing to save him so escaped using a pair of angel wings. The Advocate used Crane's death to finally destroy Matthew's faith in the Doctor and Matthew elected to instead travel with the Advocate.

This story was originally solicited as a two-parter in December 2009.[1] By January 2010, the story was described to retailers as a four-parter.[2]

Distribution problems plagued the first part of this story, and it was unusually not released across the United States on the same day. Readers on the east coast were not able to purchase Doctor Who (2009) until 24 March2010. Readers in the midwest and west got it on its intended release date, 17 March 2010.[3]

The Doctor says he "played Hamlet a little while back". David Tennant played Hamlet in a 2008 Royal Shakespeare Company production.

Several characters ask Martha if it's "Martha Jones" or "Martha Smith" now, and the Doctor says she should go back to Mickey, after which she calls him and asks if he needs help with the Sontaran problem. (TV: The End of Time)